[2024-01-24 13:22:10,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,558] [INFO] DQC Reference Directory: /var/lib/cwl/stge8f453e1-eae0-4966-90af-e2a92cb3fbfe/dqc_reference
[2024-01-24 13:22:11,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:11,896] [INFO] Task started: Prodigal
[2024-01-24 13:22:11,896] [INFO] Running command: gunzip -c /var/lib/cwl/stga5788e74-cf45-45d3-8863-9ec2db356ae6/GCF_018305205.1_ASM1830520v1_genomic.fna.gz | prodigal -d GCF_018305205.1_ASM1830520v1_genomic.fna/cds.fna -a GCF_018305205.1_ASM1830520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:16,801] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:16,801] [INFO] Task started: HMMsearch
[2024-01-24 13:22:16,801] [INFO] Running command: hmmsearch --tblout GCF_018305205.1_ASM1830520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8f453e1-eae0-4966-90af-e2a92cb3fbfe/dqc_reference/reference_markers.hmm GCF_018305205.1_ASM1830520v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:17,056] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:17,057] [INFO] Found 6/6 markers.
[2024-01-24 13:22:17,097] [INFO] Query marker FASTA was written to GCF_018305205.1_ASM1830520v1_genomic.fna/markers.fasta
[2024-01-24 13:22:17,097] [INFO] Task started: Blastn
[2024-01-24 13:22:17,098] [INFO] Running command: blastn -query GCF_018305205.1_ASM1830520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8f453e1-eae0-4966-90af-e2a92cb3fbfe/dqc_reference/reference_markers.fasta -out GCF_018305205.1_ASM1830520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:17,759] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:17,762] [INFO] Selected 17 target genomes.
[2024-01-24 13:22:17,763] [INFO] Target genome list was writen to GCF_018305205.1_ASM1830520v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:17,784] [INFO] Task started: fastANI
[2024-01-24 13:22:17,785] [INFO] Running command: fastANI --query /var/lib/cwl/stga5788e74-cf45-45d3-8863-9ec2db356ae6/GCF_018305205.1_ASM1830520v1_genomic.fna.gz --refList GCF_018305205.1_ASM1830520v1_genomic.fna/target_genomes.txt --output GCF_018305205.1_ASM1830520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:28,136] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:28,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8f453e1-eae0-4966-90af-e2a92cb3fbfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:28,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8f453e1-eae0-4966-90af-e2a92cb3fbfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:28,142] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:28,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:28,142] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Turicibacter bilis	strain=MMM721	GCA_018305205.1	2735723	2735723	type	True	100.0	864	868	95	conclusive
Turicibacter bilis	strain=MMM721	GCA_024499055.1	2735723	2735723	type	True	99.9953	868	868	95	conclusive
Turicibacter sanguinis	strain=MOL361	GCA_013046825.1	154288	154288	type	True	80.967	431	868	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:28,144] [INFO] DFAST Taxonomy check result was written to GCF_018305205.1_ASM1830520v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:28,145] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:28,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:28,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8f453e1-eae0-4966-90af-e2a92cb3fbfe/dqc_reference/checkm_data
[2024-01-24 13:22:28,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:28,179] [INFO] Task started: CheckM
[2024-01-24 13:22:28,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018305205.1_ASM1830520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018305205.1_ASM1830520v1_genomic.fna/checkm_input GCF_018305205.1_ASM1830520v1_genomic.fna/checkm_result
[2024-01-24 13:22:50,834] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:50,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:50,850] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:50,851] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:50,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018305205.1_ASM1830520v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:50,852] [INFO] Task started: Blastn
[2024-01-24 13:22:50,852] [INFO] Running command: blastn -query GCF_018305205.1_ASM1830520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8f453e1-eae0-4966-90af-e2a92cb3fbfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_018305205.1_ASM1830520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:51,688] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:51,691] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:51,691] [INFO] Target genome list was writen to GCF_018305205.1_ASM1830520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:51,702] [INFO] Task started: fastANI
[2024-01-24 13:22:51,702] [INFO] Running command: fastANI --query /var/lib/cwl/stga5788e74-cf45-45d3-8863-9ec2db356ae6/GCF_018305205.1_ASM1830520v1_genomic.fna.gz --refList GCF_018305205.1_ASM1830520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018305205.1_ASM1830520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:59,044] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:59,051] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:59,051] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_001543345.1	s__Turicibacter sp001543345	97.9261	751	868	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	98.30	97.82	0.87	0.78	10	conclusive
GCA_017888305.1	s__Turicibacter sp017888305	83.4591	394	868	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013046825.1	s__Turicibacter sanguinis	80.9605	433	868	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	99.52	99.21	0.94	0.89	18	-
GCF_009935875.1	s__Turicibacter sp002311155	80.1959	320	868	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	99.25	99.25	0.93	0.91	3	-
GCA_002493395.1	s__Turicibacter sp002493395	80.112	285	868	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003486705.1	s__Turicibacter sp003486705	78.3727	175	868	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:59,055] [INFO] GTDB search result was written to GCF_018305205.1_ASM1830520v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:59,056] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:59,058] [INFO] DFAST_QC result json was written to GCF_018305205.1_ASM1830520v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:59,058] [INFO] DFAST_QC completed!
[2024-01-24 13:22:59,058] [INFO] Total running time: 0h0m49s